+Open data
-Basic information
Entry | Database: PDB / ID: 1sws | ||||||
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Title | CORE-STREPTAVIDIN MUTANT D128A AT PH 4.5 | ||||||
Components | PROTEIN (STREPTAVIDIN) | ||||||
Keywords | BINDING PROTEIN / BIOTIN BINDING PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Freitag, S. / Chu, V. / Le Trong, I. / Klumb, L.A. / To, R. / Stayton, P.S. / Stenkamp, R.E. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: A structural snapshot of an intermediate on the streptavidin-biotin dissociation pathway. Authors: Freitag, S. / Chu, V. / Penzotti, J.E. / Klumb, L.A. / To, R. / Hyre, D. / Le Trong, I. / Lybrand, T.P. / Stenkamp, R.E. / Stayton, P.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sws.cif.gz | 98.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sws.ent.gz | 75.8 KB | Display | PDB format |
PDBx/mmJSON format | 1sws.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sws_validation.pdf.gz | 442.1 KB | Display | wwPDB validaton report |
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Full document | 1sws_full_validation.pdf.gz | 449.3 KB | Display | |
Data in XML | 1sws_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 1sws_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/1sws ftp://data.pdbj.org/pub/pdb/validation_reports/sw/1sws | HTTPS FTP |
-Related structure data
Related structure data | 1swtC 1swcS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13237.326 Da / Num. of mol.: 4 / Mutation: D128A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) Description: T7 EXPRESSION SYSTEM (PET-210, NOVAGEN, INC., MADISON,WI. SYNTHETIC GENE) Production host: Escherichia coli (E. coli) / References: UniProt: SAV_STRAV, UniProt: P22629*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 49.85 % | |||||||||||||||
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Crystal grow | pH: 4.5 / Details: 50% MPD (2-METHYL-2,4-PENTANEDIOLE), PH 4.5. | |||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 13, 1996 |
Radiation | Monochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 30500 / % possible obs: 85 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2→2.1 Å / Mean I/σ(I) obs: 2 / % possible all: 46 |
Reflection | *PLUS Num. measured all: 56045 |
Reflection shell | *PLUS % possible obs: 46 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SWC Resolution: 2→10 Å / Num. parameters: 14379 / Num. restraintsaints: 14409 / Cross valid method: RFREE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973) 201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 3230 / Occupancy sum non hydrogen: 3594 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 10 Å / σ(F): 4 / % reflection Rfree: 10 % / Rfactor obs: 0.167 / Rfactor Rwork: 0.185 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 32 Å2 |